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 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
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 *         https://www.apache.org/licenses/LICENSE-2.0.txt
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 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
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//
// This example illustrates how to explore the domain of an image metric.  This
// is a useful exercise before starting a registration process, since
// familiarity with the characteristics of the metric is fundamental for
// appropriate selection of the optimizer and its parameters used to drive the
// registration process.
// This process helps identify how noisy a metric may be in a given
// range of parameters, and it will also give an idea of the number of local
// minima or maxima in which an optimizer may get trapped while exploring the
// parametric space.
//


#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"


//
// We start by including the headers of the basic components: Metric, Transform
// and Interpolator.
//

#include "itkMeanSquaresImageToImageMetric.h"
#include "itkTranslationTransform.h"
#include "itkNearestNeighborInterpolateImageFunction.h"


#include "itkTestDriverIncludeRequiredFactories.h"
int
main(int argc, char * argv[])
{
  RegisterRequiredFactories();
  if (argc < 3)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << "  fixedImage  movingImage" << std::endl;
    return EXIT_FAILURE;
  }

  //
  // We define the dimension and pixel type of the images to be used in the
  // evaluation of the Metric.
  //

  constexpr unsigned int Dimension = 2;
  using PixelType = unsigned char;

  using ImageType = itk::Image<PixelType, Dimension>;


  using ReaderType = itk::ImageFileReader<ImageType>;

  const ReaderType::Pointer fixedReader = ReaderType::New();
  const ReaderType::Pointer movingReader = ReaderType::New();

  fixedReader->SetFileName(argv[1]);
  movingReader->SetFileName(argv[2]);

  try
  {
    fixedReader->Update();
    movingReader->Update();
  }
  catch (const itk::ExceptionObject & excep)
  {
    std::cerr << "Exception catched !" << std::endl;
    std::cerr << excep << std::endl;
  }

  //
  // The type of the Metric is instantiated and one is constructed.  In this case
  // we decided to use the same image type for both the fixed and the moving
  // images.
  //

  using MetricType = itk::MeanSquaresImageToImageMetric<ImageType, ImageType>;

  const MetricType::Pointer metric = MetricType::New();


  //
  // We also instantiate the transform and interpolator types, and create objects
  // of each class.
  //

  using TransformType = itk::TranslationTransform<double, Dimension>;

  const TransformType::Pointer transform = TransformType::New();


  using InterpolatorType = itk::NearestNeighborInterpolateImageFunction<ImageType, double>;

  const InterpolatorType::Pointer interpolator = InterpolatorType::New();


  transform->SetIdentity();

  const ImageType::ConstPointer fixedImage = fixedReader->GetOutput();
  const ImageType::ConstPointer movingImage = movingReader->GetOutput();


  //
  // The classes required by the metric are connected to it. This includes the
  // fixed and moving images, the interpolator and the transform.
  //

  metric->SetTransform(transform);
  metric->SetInterpolator(interpolator);

  metric->SetFixedImage(fixedImage);
  metric->SetMovingImage(movingImage);

  metric->SetFixedImageRegion(fixedImage->GetBufferedRegion());

  try
  {
    metric->Initialize();
  }
  catch (const itk::ExceptionObject & excep)
  {
    std::cerr << "Exception catched !" << std::endl;
    std::cerr << excep << std::endl;
    return EXIT_FAILURE;
  }


  //
  // Finally we select a region of the parametric space to explore. In this case
  // we are using a translation transform in 2D, so we simply select translations
  // from a negative position to a positive position, in both $x$ and $y$. For
  // each one of those positions we invoke the \code{GetValue()} method of the Metric.
  //

  MetricType::TransformParametersType displacement(Dimension);

  constexpr int rangex = 50;
  constexpr int rangey = 50;

  for (int dx = -rangex; dx <= rangex; ++dx)
  {
    for (int dy = -rangey; dy <= rangey; ++dy)
    {
      displacement[0] = dx;
      displacement[1] = dy;
      const double value = metric->GetValue(displacement);
      std::cout << dx << "   " << dy << "   " << value << std::endl;
    }
  }


  //
  // \begin{figure}
  // \center
  // \includegraphics[height=0.33\textwidth]{MeanSquaresMetricPlot1}
  // \includegraphics[height=0.33\textwidth]{MeanSquaresMetricPlot2}
  // \itkcaption[Mean Squares Metric Plots]{Plots of the Mean Squares Metric for
  // an image compared to itself under multiple translations.}
  // \label{fig:MeanSquaresMetricPlot}
  // \end{figure}
  //
  // Running this code using the image BrainProtonDensitySlice.png as both the
  // fixed and the moving images results in the plot shown in
  // Figure~\ref{fig:MeanSquaresMetricPlot}. From this figure, it can be seen
  // that a gradient-based optimizer will be appropriate for finding the extrema
  // of the Metric. It is also possible to estimate a good value for the step
  // length of a gradient-descent optimizer.
  //
  // This exercise of plotting the Metric is probably the best thing to do when a
  // registration process is not converging and when it is unclear how to fine
  // tune the different parameters involved in the registration. This includes
  // the optimizer parameters, the metric parameters and even options such as
  // preprocessing the image data with smoothing filters.
  //
  // The shell and Gnuplot\footnote{http://www.gnuplot.info} scripts used for
  // generating the graphics in Figure~\ref{fig:MeanSquaresMetricPlot} are
  // available in the directory
  //
  //             \code{ITKSoftwareGuide/SoftwareGuide/Art}
  //
  // Of course, this plotting exercise becomes more challenging when the
  // transform has more than three parameters, and when those parameters have
  // very different value ranges. In those cases it is necessary to select only a
  // key subset of parameters from the transform and to study the behavior of the
  // metric when those parameters are varied.
  //
  //


  return EXIT_SUCCESS;
}
